If you’re working with molecular docking, structural analysis, or simulations across many proteins, you’ve likely run into this challenge: preparing dozens or even hundreds of raw PDB files manually. Stripping water, removing unnecessary ligands, adding hydrogens, resolving alternate locations… doing this for one structure is manageable. But repeating those steps dozens of times? That’s tedious and error-prone.
Fortunately, SAMSON offers a solution designed for high-throughput molecular modelers: the Batch Protein Prepare extension. Whether you’re screening binding sites or setting up a library for docking, this tool can save significant time and reduce inconsistencies across datasets.
Why Batch Preparation Really Helps
Unlike single-structure prep workflows, Batch Protein Prepare is designed for scale:
- Automate repetitive clean-ups: Eliminate solvents, redundant ligands, ions, and more using the same criteria across all files.
- Streamline with a few clicks: Apply the full SAMSON preparation protocol to dozens of proteins without opening them manually.
- Preserve folder structures: Get cleaned output neatly organized just like your inputs were.
- Accepts multiple input types: PDB, mmCIF/PDBx, MMTF, and MOL2 files are all supported.
- Fetch directly from PDB: Input a list of PDB identifiers to automatically download and prepare structures—no manual downloading required.
How It Works
The Batch Protein Prepare extension is available through SAMSON’s Extension Store. Once installed, you can launch it from within the platform. Here’s what the workflow typically looks like:
- Select a folder containing your raw structure files, or provide a text list of PDB codes.
- Decide whether to strip water, ions, and ligands, add hydrogens, resolve alternate locations, etc.
- Click “Run” and let SAMSON process all files with the selected options.
The output will be clean, validated protein structures—ready to use in docking, MD simulation, or other modeling workflows.
Best Use Cases
- Docking screen setup: Prepare dozens of receptors or co-crystal structures before virtual screening.
- Library curation: If you’re assembling a curated dataset of protein-ligand systems for ML or benchmarking.
- Model validation studies: Standardize input for comparative evaluations across datasets.
Things to Keep in Mind
- Batch preparation applies uniform criteria. Be sure those criteria work well for all structures in the folder.
- Hydrogens are added based on residue type. If you need pH-specific protonation states, complement this step with PDBFixer (also available in SAMSON).
For modelers balancing accuracy and efficiency, the Batch Protein Prepare extension can be a valuable step in your workflow. It’s designed to help you spend less time clicking and more time analyzing.
To learn more about preparing proteins in SAMSON, including details on batch preparation, visit the full documentation: https://documentation.samson-connect.net/tutorials/prepare-protein/prepare-protein/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.